European Master's Program in Computational Logic

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17 December 2013

Master Thesis Defense by Ms Alina Petrova

Ms Alina Petrova defended her master thesis on 'Learning formal definitions for biomedical concepts'


Ms Alina Petrova defended her master thesis on 'Learning formal definitions for biomedical concepts' on 6 December 2013 at TUD.

Abstract:

Ontologies play a major role in life sciences, enabling a number of applications, from new data integration to knowledge verification. Obtaining formalized knowledge from unstructured data is especially relevant for biomedical domain, since the amount of textual biomedical data has been growing exponentially. The aim of this thesis is to develop a method of creating formal definitions for biomedical concepts using textual information from scientific literature (PubMed abstracts), encyclopedias (Wikipedia), controlled vocabularies (MeSH) and the Web. The knowledge representation formalism of choice is Description Logic as it allows for integrating the newly acquired axioms in existing biomedical ontologies (e.g. SNOMED) as well as for automated reasoning on top of them. The work is specifically focused on extracting non-taxonomic relations and their instances from natural language texts. It encompasses the analysis, description, implementation and evaluation of the supervised relation extraction pipeline and sets the scene for the unsupervised relation extraction, proposing a novel algorithm of relation discovery via semantic clustering.